Yes, I'm afraid that's not it. I only have one workspace so far.
Short update: The first app that I created was a packaged application, on install it automatically got the ID 116 (quite strange...) The next applications I created got the numbers 100, 101 and 102 (It was recommended as a preset, I didn't change it.) Now I created another app with the ID 118, and it shows up in the "apex_applications" view. I double checked, only applications with an id higher than 115 show up in the view, the rest doesn't.
I deleted application 116, thinking that it is somehow corrupted, but it did not help. Maybe there are some entries left somewhere.